PHY480 - Computational Physics
Instructor Phil Duxbury (BPS 4260, duxbury at pa.msu.edu)
TAs Connor Glosser, Nan Du
First lecture: 6-7pm Wednesday Jan. 16 or 2-3pm Friday Jan. 18 (choose one) BPS1240
Lecture times Lecture 6-7pm Wednesday, 2-3pm Friday (same lecture twice) BPS1240
Laboratory times when TAs or lecturer will be there 6-9pm Wednesday, 2-6pm Friday, BPS1240
Additional times when BPS1240 will be open TBA
Coding notes: Read this first!
A must read: Programming notes for the ICCP,
including brief introduction to coding and unix - mostly Fortran but also some thoughts about other languages
The international option is in collaboration with
Technical University Delft, in Delft the Netherlands. In the international option
coding may be done in either C++ or Fortran 90, the choice being made by
each group of students.
Co-instructor for the International option: Prof. Jos Thijssen.
This course emphasises developing Fortran code and using it to simulate
several different systems of broad interest in physics. Students may also use C++/python but
the coding discussions will mostly be based in Fortran. The main
projects are based on the following methods / problems which form the basis of
Monte Carlo Methods.
Molecular Dynamics Methods
Getting to know Fortran:
To get started do the first two worksheets in the
introduction to fortran course. There you will find a summary of Fortran syntax,
some examples and a more comprehensive introduction to Fortran 90. A summary
of linux commands is also there.
Deadline for report: 6pm Friday 22nd February.
MC methods I and Outline of the first project
MC methods II
You should write your report in latex with the figures
embedded in the text. Here is a template to use.
This contains a figure and is called in such a way that the
figure needs to be in the same directory as the .tex file. Here is the figure.
To create a .pdf file from the .tex file you only need to enter "pdflatex mclecture1.tex"
to create a file called mclecture1.pdf. There are many good online introductions
to latex. One aspect not required for the first project report is the
use of a bibliography file. That will be introduced in the second
First project: ICCP - MD for Argon
Deadline for ICCP report: 6pm Friday 22nd February.
The report Each person may write their own report, using
the same data as their partners. Alternatively a joint report
with the dutch partners is acceptable, provided you understand
and participate in writing all parts of the report. The report should be
written in .tex. Please send a copy of your report (.pdf) and
a copy of your code by email.
Link to second ICCP projects
Second project: PHY480, Not-ICCP - MD for Argon - Due April 7th (writeup in .tex, using .bib file)
Background that you might find useful.
Introduction to MD and outline of the second project.
A fortran 90 code for MD simulation of two particles in LJ potential
A fortran 90 code to generate an fcc lattice
A Mathematica code to visualize the fcc lattice
More information on the MD project and some useful coding tricks.
Third Project - Both PHY480 and ICCP: Due May 3
Here is a summary of the four options available for the third project
Background for each of the four options is as follows:
Tight binding project (Option 1);
on tight binding for graphene.
A paper on localization in quantum percolation.
A paper on localization in the Anderson model.
a review of localization
The Quantum Spin Chain Problem (Option 2)
The Schrodinger Dynamics Problem (Option 3)
Lattice Boltzmann (Option 3.5)
For each project you will write a report, which contains
the objective of the calculations, your code, and the results you generated
using your code. These reports constitute 75% of the grade. There will be a 1 hour final
lab exam based on your projects. . These meetings will be held
in BPS1240. During your "final" meeting we will discuss your project reports and codes that
you hand in, and you will be asked to run your algorithms to illustrate
some issues. In addition you will be asked to make relatively minor modifications
of your codes to calculate new things.
PHY201 - introduction
to fortran. This is the introductory Fortran course. The worksheets have some sample
Fortran 90 reference card
Here is a more complete
summary of Fortran 90 which we shall refer to during the course. It comes from the
Here is a list of
useful unix commands and an introduction to
Linux Computing in BPS1240.
The worksheets for the
PHY201 might be also useful
Computational phyiscs, J.M. Thijssen (Cambridge University Press,1999)
Other useful books
Introduction to computer simulations methods, Second Edition.
H. Gould and J. Tobochnik (Addison-Wesley,1996)
Molecular modeling for beginners, A Hinchcliffe (Wiley,2003)
"An introduction to Fortran 90 for scientific computing", by James M. Ortega.
A more advanced book is
"Fortran 90/95 explained" second edition. by Michael Metcalf and
John Reid. Oxford University Press, 1999.
A nice (free) online book containing Fortran 77, Fortran 90 and C++ codes for
a wide range of useful procedures is
Numerical recipes online . They are charging for later editions.
Some other useful links
Python reference card
C++ reference card
Michael Feig's Lecture notes on biomolecular
simulations using CHARMM. Read this to learn how to define the energy functions.
Review of Monte Carlo
Methods for proteins (.pdf file). Read this to learn how to choose the Monte Carlo moves.
The rational behind force fields
The CHARMM22 force field for proteins
Review of simulation
methods for macromolecules by Kurt Kremer (.pdf file)
c++ or f90 - you make the call
C++ or Fortran for scientific computing
f90 is better, including efficiency comparisons